[Chimera-users] Creating a single pdb file from multiple pdb files

Steven Bottomley S.Bottomley at curtin.edu.au
Wed Jan 25 18:42:20 PST 2012

Thanks to both Elaine and Darrell for your help!

I also learned from the developer that Yasara Dynamics can average proteins using the AveragePos command.


On 25/01/2012, at 1:47 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> Hi there,
> I've just been doing this myself. In general, it is not a good idea to
> average structures for analysis, but I'm doing it for illustrative
> purposes.
> I followed the lead on this page:
> http://www.zelleke.com/2011/02/get-an-average-structure-from-your-trajector
> y/
> I use VMD to create an "averaged" structure, but the geometry of side
> chains sometimes get messed up. So after doing the VMD thing, I run a
> Rosetta "idealize":
> http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_ide
> alize.html
> Once you have everything set up, the calculations take only a few minutes.
> Maybe that will help someone!
> Cheers,
> Darrell
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office  301-402-0095
> Mobile 301-758-3559
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> On 1/24/12 11:50 AM, "Elaine Meng" <meng at cgl.ucsf.edu> wrote:
>> Hi Steven,
>> Sorry, currently there is nothing in Chimera to calculate average
>> structures.  Chimera's "Ensemble Cluster" tool will identify clusters and
>> representative structures from ensembles (where each structure has the
>> same atoms, just different coordinates), but it doesn't calculate
>> averaages.
>> I was looking at the chimera-users list archive on this topic and saw
>> that somebody had recommended the following:
>> <http://structbio.vanderbilt.edu/~jsmith/suppose/>
>> I haven't tried it, however.  Best,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D.
>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> On Jan 24, 2012, at 3:27 AM, Steven Bottomley wrote:
>>> Hi
>>> It is possible to create a single (preferably weighted) protein
>>> structure (pdb file) from two or more related protein structures (pdb
>>> files)? I guess that this would be something like creating a single
>>> (weighted average) of NMR ensemble structures but using any chosen pdb
>>> file. Thanks for any help!
>>> Regards
>>> Steven
>> _______________________________________________
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>> Chimera-users at cgl.ucsf.edu
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Dr Steven Bottomley
Unit Coordinator, and lecturer, for Biochemistry 233, Biochemistry 234, Structural Bioinformatics 332, and Molecular Techniques 632 | School of Biomedical Sciences | Faculty of Health Sciences

Curtin University
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Email | mailto: s.bottomley at curtin.edu.au
Web | http://curtin.edu.au

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